sawfish v0.12.8

v0.12.8 - 2024-12-13

Fixed

• Increase system open file limit (github #9)
  • May simplify joint-call for large pedigrees at high thread counts
• Improve error message when split reads map to an unknown chromosome (github #8)

sawfish v0.12.7

v0.12.7 - 2024-10-23

Fixed

• Fix "Illegal Instruction" error reported for some use cases (github #3)
  • Removed gcc native cpu optimization in WFA2-lib believed to be causing this issue
  • Added additional --debug output to discover mode contig alignment logic

sawfish v0.12.6

v0.12.6 - 2024-10-15

Fixed

• Fix discover mode input path canonicalization (reversed flag logic)

sawfish v0.12.5

v0.12.5 - 2024-10-14

Added

• Add new joint-call --report-supporting-reads option to report read names supporting each variant

Changed

• CR-390 Canonicalize all discover mode input paths
  • Also provide new --disable-path-canonicalization discover step option to store input paths as-is
• CR-391 Don't create output directory until command line is validated

sawfish v0.12.4

v0.12.4 - 2024-09-13

Added

• CR-384 Add debug logging option
  • High detail level intended to improve crash reports from external users
  • Initially populated for breakpoint refinement only, debug log coverage will be expanded as required
• Expose clobber option to overwrite existing output directory

Fixed

• CR-385 Improve error message for unexpected alignment patterns from VACmap
  • This also adjusts some off-by-one errors in neighbor extension handling, which could cause infrequent changes to inversion output
  • Note VACmap is still unsupported; working towards clear error messages for problematic alignments from any source

sawfish v0.12.3

v0.12.3 - 2024-09-03

Fixed

• CR-378 Improve error message for hard-clipped split read input
• CR-379 Improve error message when discover directory is missing

sawfish v0.12.2

v0.12.2 - 2024-08-21

Fixed

• CR-377 Remove rq tag requirement in input alignment records

sawfish v0.12.1

v0.12.1 - 2024-08-08

Fixed

• CR-375 Fix infrequent discover mode failures due to invalid breakpoint ranges.
  • Issue seems to have started with v0.12.0 via CR-340

sawfish v0.12.0

v0.12.0 - 2024-05-23

Added

• CR-327 Add local SV phasing
  • Short-range phasing provided in VCF records wherever multiple hets are genotyped on one or more overlapping SV haplotypes

Changed

• CR-340 Improve handling of multi-breakpoint haplotypes
  • Improves detection of complex SV breakpoints, especially for small inversions
• CR-333 Adjust alignment for long breakpoint homology
  • Improves detection of high homology inversions
• CR-330 Expand trimmed read search region for small SV regions
  • Improves detection of soft-clipped evidence for low homology insertions

sawfish v0.11.0

v0.11.0 - 2024-04-18

Improve a number of discovery and scoring features related to inversions, inverted breakpoints and large deletions.

Changed

• CR-323 Improve scoring for a number of cases relevant to inversions and inverted breakpoints
• CR-321 Change contig flank size handling to improve large inversion calling
• CR-318 Expand trimmed read search region for large SV candidates
  • Improves recall for inverted breakpoints and duplications
• CR-317 Standardize on csi indexing for bam output

Fixed

• CR-324 Fix non-deterministic inversion output